BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge
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- 作者：Emilio Gallicchio ; Haoyuan Chen ; He Chen…
- 关键词：Binding energy distribution analysis method ; Implicit solvation ; Analytic generalized Born plus non ; polar model ; Blind prediction
- 刊名：Journal of Computer-Aided Molecular Design
- 出版年：2015
- 出版时间：April 2015
- 年：2015
- 卷：29
- 期：4
- 页码：315-325
- 全文大小：934 KB
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文摘
The binding energy distribution analysis method (BEDAM) protocol has been employed as part of the SAMPL4 blind challenge to predict the binding free energies of a set of octa-acid host–guest complexes. The resulting predictions were consistently judged as some of the most accurate predictions in this category of the SAMPL4 challenge in terms of quantitative accuracy and statistical correlation relative to the experimental values, which were not known at the time the predictions were made. The work has been conducted as part of a hands-on graduate class laboratory session. Collectively the students, aided by automated setup and analysis tools, performed the bulk of the calculations and the numerical and structural analysis. The success of the experiment confirms the reliability of the BEDAM methodology and it shows that physics-based atomistic binding free energy estimation models, when properly streamlined and automated, can be successfully employed by non-specialists.